The controversial decision by Natural England to extend the culling of badgers in Gloucestershire was narrowly approved against the recommendation of its own top scientific adviser, according to internal documents seen by the Guardian.

At the board meeting, the head of NE's science advisory committee, Professor David Macdonald, described the view that killing more badgers would lead to better disease control was "not easily reconciled with the evidence".

The nation's official wildlife body, granted the extension without seeking independent advice and against Prof Macdonald's guidance, the minutes of an NE board meeting record.

A legal challenge to abandon the cull is now certain, said the Badger Trust, which successfully ended culling in Wales through court action.

The NE executive who made the final decision to extend the cull, Andrew Wood, told the meeting: "The science was uncertain and did not give a definitive answer. A judgement-based decision had to be made."

Prof Macdonald, an NE board member and badger expert, told the Guardian: "It's an appalling dilemma, but the evidence suggests an extension of the culling in Gloucestershire is unlikely to [curb tuberculosis in cattle]. I fear there will be two tragic losers, the farmers who are paying the crippling bill for extending this trial and the badgers whose lives may be lost for little purpose"

Jeff Hayden, a director at the Badger Trust, said: "This government has a feudal attitude to wildlife and feudal attitude to transparency. They have withheld information as long as possible and have still not disclosed other information. We will make the legal challenge, it is just a matter of timing."

The badger culls in Somerset and Gloucestershire are intended to test whether shooting free-running badgers at night can kill enough animals to cut TB infections in cattle. Both failed to kill the minimum 70% required in the six weeks allowed but both were granted extensions by NE. Even after its extension, the Somerset cull still failed to meet its minimum target. Bovine TB has risen in the last decade and led to the slaughter of 28,000 cattle in 2012, which ministers say cost taxpayers £100m.

The NE board meeting on 23 October considered the case for extending the Gloucestershire cull by eight weeks, but four of the nine members expressed severe reservations, particularly on the pivotal advice of the government's chief veterinary officer (CVO) Nigel Gibbens. Wood said that advice was "the key" to the decision to extend.

During the meeting, the minutes of which have been obtained by the Guardian, MacDonald said: "The CVO's advice that killing further badgers would lead to better disease control is not easily reconciled with the evidence." He added it was "hard to understand" how further trials could be licensed following the failure of the initial culls. Other board members agreed that the extension was likely to increase TB infections in cattle, with one noting "independent advice should have been sought". The minutes record discussion of "the fact that it was difficult to predict what the disease control benefits would be". In the end, the board voted narrowly to allow Wood to make the decision.

A decade-long project that ended in 2008, called the randomised badger culling trial (RBCT), found that killing over 70% of badgers for several years curbed TB by about 16%. But it concluded that culling under 30% of badgers actually led to an increase in TB infections in cattle, as fleeing badgers spreading TB more widely, an effect called perturbation.

In the first six weeks of the Gloucestershire cull, only 30% of badgers were shot, even after a drastic cut in the badger numbers initially estimated to live in the area. The NE minutes, marked "restricted – in confidence", reveal that "part of the Gloucestershire culling area had been inaccessible due to protester activity." In the RBCT, the badger culls were conducted over far shorter periods: 8-11 days to reduce the risk of perturbation.

Gibbens's advice to NE, based on the RBCT data, was that extending the culling for another eight weeks would reduce TB in cattle. However, a core member of the team that conducted the RBCT, Prof Rosie Woodroffe said: "The chief vet's advice to carry on culling is based upon a very incomplete view of the available evidence. The targets were set high for a reason – if you don't get enough badgers, you make things worse." The scientist who commissioned the RBCT, Lord John Krebs, has called the culls "mindless".

MacDonald said: "My biggest concern is a higher level issue that transcends the case of badgers, and I am deeply concerned that 'advice' from Defra officials should have such a determining effect on the decisions of [Natural England] whose function is independently to evaluate evidence. It is crucial that government should have the benefit of constructive challenge from non-departmental bodies that are sufficiently well-resourced and independent to give the highest calibre of advice." In September, deputy prime minister Nick Clegg revealed that he had blocked attempts by his Conservative coalition partners to scrap NE.

An NE spokesman said: "There are obviously going to be different individual views expressed during meetings. The executive has granted the cull extensions with the full authority of the board and taking account of the very clear advice of the CVO that this would have net disease control benefits."

A Defra spokesman said: "NE's experts carefully considered all the information and recommended the licence to continue culling should be granted. This was in line with the CVO's advice, which has been backed by the British Veterinary Association. We need to do everything we can to get on top of bovine TB which is spreading across the country and devastating our cattle and dairy industries."